Welcome to the BIDS_coding Documentation

This is the main page of the BIDS_coding documentation. Here you will find the table of contents and links to other important resources.

User Guide:

• Data2BIDS
  • Named Arguments
  • Global Local

Useful Links

• BIDS_coding @ GitHub
• Issue Tracker
• Wiki

Work in Progress

See issues for updates on code completion progress

BIDS_coding

These scripts are intended for the creation and manipulation of BIDS compliant IEEG data set to the new specifications. Currently focused on EEG data type conversion, although multi-echo MRI data is also supported. For more conventional fMRI type BIDS conversions it is recommended you first look at BIDScoin as it has great general coverage than this repository.

Each python script can be run repreatedly using an iterator shell script like the one within the bids converter. They can also be run in the command line and will automatically iterate through a whole dataset if the top folder is indicated in the command.

BIDS_converter methodology is based off of this project

Dependencies

Software (as needed only): Afni, Freesurfer, Fsl, Anaconda (python 3.8)

Python packages:

boto3, pathlib, pybids, pydicom, nipype, pip, tedana, scipy

Optional python packages

bids-validator

Ubuntu packages:

dcm2niix, pigz

Host Requirements

Linux:

xauth

Mac:

xQuartz

The Lab

https://www.coganlab.org/

Indices and Tables

• Index

• Module Index

• Search Page

• MATLAB Module Index

Thank you for using BIDS_coding!